This is one of the most likely things you'll find in common with anime which physically takes place in Japan.

As I've been to Japan several times already I cannot say what I think is, but I'll try my best at pointing out some things I've seen in anime which are quite close to reality in daily life.
Minor things I have noticed while traveling through Japan which I've also seen in anime are people sleeping on the subway (very common), salaryman in Izakaya (Japanese pubs) and their quite typical behaviour (extremely common), morning and evening commutes (Avoid, AVOID! No seriously you do NOT want to be in a train during those!), Shibuya crossing (people, people everywhere!!) and back when I was a smoker myself, Japanese smoking habbits.
(Most Japanese people I've seen smoking never finish a whole cigarette, they smoke half or take a few puffs before extinguishing it and moving on or lighting the next. In a lot of anime with smoking characters the exact same happens. I was the one getting weird looks, well because I was a big European foreigner of course, but also because I finished the whole cig. )

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